AMBER Archive (2008)

Subject: Re: AMBER: High Bfactor values for the terminal residues/atoms

From: Carlos Simmerling (
Date: Tue Oct 14 2008 - 05:25:25 CDT

do you see a lot of motion in them when you visually inspect the
dynamics in a program such as VMD?
I use my eyes to figure out what's going on, and ptraj to quantify it.

On Tue, Oct 14, 2008 at 12:19 AM, Siddharth Rastogi
<> wrote:
> Dear ALL,
> While calculating Bfactor values, I observe very large values for the end
> terminal residues in particular.
> This is the input I have given
> trajin wtld.mdcrd.gz
> center :1-n
> image center familiar
> rms first :1-n_at_CA
> atomicfluct out wtld_bfactor_residue @CA byres bfactor
> can anyone suggest me where I might have done wrong.
> regards,
> Siddharth Rastogi
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